After shakedown off the California coast, Silversides set course for Hawaii, arriving at Pearl Harbor on 4 April 1942. Departing Pearl Harbor on 30 April, Silversides headed for the Japanese home islands, in the area of Kii Suido, for the first of her many successful war patrols. On 10 May, just after 08:00 local time, the submarine heavly a Japanese gunboat with her three-inch (76 mm) gun. During this 75 minute action, an enemy machine-gun bullet killed one of her deck gunners, TM3 Mike Harbin, the only man to perish on the top deck of a submarine during World War II. Harbin was buried at sea later that evening. On 13 May, Silversides torpedoed an enemy submarine; but, although explosions were heard, a definite sinking could not be confirmed.
On 17 May, Silversides torpedoed and sank a 4000-ton cargo ship and damaged a second in one of the more interesting engagements of the war. While maneuvering through an enemy fishing fleet and approaching the cargo ships, the submarine's periscope became entangled in a fishnet marked by Japanese flags held aloft on bamboo poles. Silversides bored in on the ill-fated enemy ships, fishnet and all, and fired three torpedoes at the first ship, with two hits that tore her stern open. While that ship was sinking, the second cargo ship was also hit, but its fate could not be determined. Patrol boats were closing in as the submarine, probably the only American submarine to make an attack while flying the Japanese flag, quickly left the vicinity. After damaging a freighter and tanker in the same area, Silversides terminated her first war patrol at Pearl Harbor on 21 June.
Silversides’s second war patrol was also conducted in the area of Kii Suido, from 15 July to 8 September. On 28 July, she sank a 4000-ton transport, followed by the sinking of the passenger-cargo ship Nikkei Maru on 8 August. She scored damaging hits on a large tanker on the night of 14 August and, on 31 August, sank two enemy trawlers before returning to Pearl Harbor.
Although there were no confirmed sinkings during Silversides’s third war patrol, conducted in the Caroline Islands, the submarine did severe damage to a large cargo ship and gained two observed torpedo hits on a Japanese destroyer or light minelayer for undetermined damage. She terminated her third patrol at Brisbane, Australia, on 25 November.
Silversides departed Brisbane on 17 December and set course for New Ireland for her fourth war patrol. While far out at sea on the night of Christmas Eve, the submarine's pharmacist's mate, PM1 Thomas Moore, performed a successful emergency appendectomy on FM2 George Platter, using ether as anaesthesia and using rudimentary tools primarily fashioned from kitchen utensils. With the operation over at 04:00 on 25 December, the submarine surfaced only to be immediately forced down by a Japanese destroyer and compelled to endure a severe depth charge attack. Thinking herself safe, Silversides surfaced only to find the destroyer still there. In addition, a Japanese airplane had arrived on the scene, and proceeded to drop three bombs on the submarine, severely damaging her bow planes and causing them to lock on full dive. Silversides managed to level off just short of crush depth and eventually evaded the enemy ship before surfacing to recharge her batteries and effect emergency repairs.
While off Truk on 18 January 1943, Silversides torpedoed and sank tanker Toei Maru. Two days later, the submarine had one of her most productive days of the war. After paralleling a convoy throughout the daylight hours, she moved on ahead at sundown to lay in wait. As the targets moved into range, she fired her torpedoes at overlapping targets and sank three enemy ships—the cargo ships Surabaya Maru, Somedono Maru, and Meiu Maru. The attack had scarcely abated when it was discovered that an armed torpedo was stuck in a forward torpedo tube. Since it was impossible to disarm the torpedo, the commanding officer decided to attempt to refire it, an extremely dangerous maneuver. The submarine moved in reverse at top speed and fired. The torpedo shot safely from the tube, disappearing as it moved toward the horizon.
When a serious oil leak was discovered later that night, the submarine left the patrol area two days ahead of schedule and returned to Pearl Harbor on 31 January.
Silversides’s fifth war patrol commenced on 17 May and was conducted in the Solomon Islands area. Her primary mission was to lay a minefield in Steffan Strait, between New Hanover and New Ireland, but she did not neglect enemy shipping. On the night of 10 June and 11 June, she sank the 5256-ton cargo ship Hide Maru; but, for her efforts, was forced to endure a severe, though fruitless, depth charging. She returned to Brisbane for refit on 16 July.
For her sixth war patrol, from 21 July to 4 September, Silversides patrolled between the Solomon Islands and Caroline Islands. Since she was plagued with malfunctioning torpedoes and a scarcity of targets, she returned to Brisbane empty-handed.
Silversides set sail on 5 October for her seventh war patrol in which she sank four enemy ships in waters ranging from the Solomon Islands to the coast of New Guinea. On 18 October, she torpedoed and sank the cargo ship Tairin Maru, and, on 24 October, made a series of daring attacks to send the cargo ships Tennan Maru and Kazan Maru and the passenger-cargo ship Johore Maru beneath the waves. She returned to Pearl Harbor for refit on 8 November.
Silversides patrolled off the Palau Islands for her eighth war patrol where, on 29 December, she brought havoc to an enemy convoy of cargo ships, sinking Tenposan Maru, Shichisei Maru, and Ryuto Maru. She terminated her eighth patrol at Pearl Harbor on 15 January 1944.
For her ninth war patrol, Silversides departed Pearl Harbor on 15 February and set course for waters west of the Marianas Islands. On 16 March, she sank the cargo ship Kofuku Maru; but, since the remainder of the patrol was void of worthwhile targets, the submarine returned to Fremantle on 8 April.
While on her tenth war patrol, off the Marianas Islands, Silversides destroyed six enemy vessels for a total of over 14,000 tons. On 10 May, she torpedoed and sank the cargo ship Okinawa Maru, followed up with the passenger-cargo ship Mikage Maru; and then sent the converted gunboat Choan Maru Number Two beneath the waves. Ten days later, she added to her score when she sank another converted gunboat, the 998-ton Shosei Maru. On 29 May, the submarine torpedoed and sank the cargo ships Shoken Maru and Horaizan Maru; and then headed for Pearl Harbor, arriving on 11 June. Two days later, she got underway for Mare Island Navy Yard for overhaul, returning to Pearl Harbor on 12 September.
Silversides set sail on 24 September for her eleventh war patrol, conducted off Kyūshū, Japan. Although this patrol was unproductive, she aided in the rescue of a stricken sister submarine. had been badly damaged in a severe depth charging and was forced to surface and try to escape while fighting enemy escorts in a gun battle, a task for which a submarine is badly outmatched. The gunfire flashes brought Silversides to the scene. She deliberately drew the attention of some of the escorts, then quickly dove to escape the gunfire. Soon, submarines and joined in helping Silversides to guard Salmon, and in escorting the stricken submarine back to Saipan, arriving on 3 November. Silversides terminated her eleventh patrol at Midway Island on 23 November.
Silversides’s twelfth war patrol commenced on 22 December and was spent in the East China Sea. Despite aggressive search, she found few worthwhile targets. However, when an opportunity did come her way, Silversides took full advantage. On 25 January 1945, she slammed home torpedoes to sink the 4556-ton cargo ship Malay Maru. She returned to Midway Island on 12 February.
During her thirteenth war patrol, Silversides was a member of a coordinated attack group with submarines and , patrolling off Kyūshū. Although she again found few worthwhile targets, the submarine did manage to damage a large freighter and to sink a trawler before returning to Pearl Harbor on 29 April.
Silversides’s fourteenth and final war patrol began with departure from Pearl Harbor on 30 May. This patrol was spent on lifeguard station in support of air strikes on Honshū, Japan. On 22 July, she rescued a downed fighter pilot from the light aircraft carrier , and two days later recovered a downed United States Army Air Corps airman. She ended this patrol at Apra Harbor, Guam, on 30 July. The submarine was undergoing refit there when the hostilities with Japan ended on 15 August.
Silversides transited the Panama Canal on 15 September, arriving at New York City on 21 September. After shifting to New London, Connecticut, she was decommissioned on 17 April 1946 and placed in reserve until 15 October 1947, when she was placed in service as a training ship for naval reservists at Chicago, Illinois. After a 1949 overhaul, she remained at Chicago for the rest of her service.
Last time the Silversides was dry-docked was after the war, in 1949, when the submarine went into the reserve fleet and its solid brass propellers were removed.
On 6 November 1962, Silversides was reclassified as an auxiliary submarine with hull classification symbol AGSS-236, and on 30 June 1969 her name was struck from the Naval Vessel Register. The South Chicago Chamber of Commerce promptly applied to the United States Department of the Navy for custody of Silversides to preserve her as a memorial. During the mid-1980s, the Silversides was docked at Chicago's Navy Pier.
Silversides became a part of the Combined Great Lakes Navy Association in Chicago, Illinois, behind Chicago's Naval Armory on 24 May 1973 and has suffered from poor management since. For years, the submarine was tended by a small crew of dedicated volunteers, drawn to her illustrious history and technical marvels. They donated tens of thousands of man-hours to restore her, maintained her at their own expense, and served as docents and chaperones. When association volunteers first stepped on board, they faced a musty, mildewed sub with paint peeling off in sheets inside and out, and junk scattered everywhere. After many years, the refrigeration compartment had produced a growth of anaerobes so thick, they could be measured in multiple inches instead of millimeters. Evidence of water damage prevailed in the forward compartments but the aft end was in reasonably good condition. Topside, the decking was weathered and worn in spots and some areas of the superstructure were rusted and in need of replacement.
A small crew of restoration volunteers was organized and quickly took steps to stop the decay. Rotted lines were replaced and the boat resecured to the pier, the bilges were pumped dry, electric power and heat were brought on board and a leak in the No. 3 torpedo tube sealed off. The first major renovation completed was stripping, undercoating and repainting the hull to the water line. The job took several months, with a break over the winter, but once completed, the Silversides looked nearly new. Below decks, the boat was cleaned and general restoration got under way. Considerable rewiring was done to bring light to all areas of the boat, the plumbing underwent investigation for leaks sprung in once-frozen pipes and a crew set about surveying the Fairbanks Morse 38D8 1/8 nine-cylinder, , opposed-piston engines. The seven-cylinder auxiliary engine was brought back to life in 1975.
She was moved to Navy Pier in 1979. That July, the first main engine, No. 3, was brought back to life for the first time since 1946. The No. 4 engine was restored in time for the 1984 U.S. Submarine Veterans of World War II convention.
From 1979 through the mid-1980s, the submarine's operators added revenue-generating tugs and survey boats to the museum's inventory without the city's permission. Further, a city investigation revealed that the operators intentionally deflated tourist counts and revenue. Because of this, city officials saw the Silversides and her "fleet" as a commercial business operating under the guise of a nonprofit organization and began to seek $30,000 back rent for pier space. The Illinois Attorney General's office also launched an investigation into the group's finances in 1985. Questions also were raised about allegations that museum management was receiving government surplus equipment for free or reduced cost then selling it at a personal profit for one individual.
Furthermore, supplies vital to the preservation of the Silversides were rarely made available to volunteers. Additionally, the chairman, president and executive director expressed blatant contempt toward the will of the frontline volunteers and a disrespect of their talent and time. These volunteers were frequently taunted, harassed and physically threatened by members of the board of directors and operating staff, until the board decided a volunteer restoration crew no longer was needed in 1985. Management was unable to develop a long-term relationship with the city of Chicago and the boat was moved to Muskegon on 7 August 1987. As further proof, two pallets of unused Rust-Oleum paint moved along with the submarine (volunteers had bought their own) it was found that teak wood donated to replace the old deck had been stolen and sold by the management.
The city announced plans to renovate Navy Pier, buoyed by a $150 million state bond issue, while the Chicago Maritime Society revealed that it would build a new museum. Both plans were without the Silversides. The U.S. Navy, watching these developments, and initially put the brakes on any move but reversed itself and allowed it.
Different management brought No. 1 and No. 2 engines on line by Labor Day 1991. Parts and equipment salvaged from scrapped fleet submarines and stored beneath the weather deck and inside her below decks compartments were removed to storage sites on shore. The familiar dark-green linoleum was replaced throughout below decks. Crew's bunks in the after battery compartment were fitted with new vinyl covers.
But the management is unable to work below the waterline. Her material condition began to deteriorate in the early years of the 21st century; her bottom needed sandblasting and repainting as well as a protective recoating.
Normally, United States Navy submarines are dry-docked every five years while on active duty. If permanently moored in fresh water the maintenance interval can be extended to 25 years. In 2004, 55 years after Silversides’s last dry-docking, the museum and two submarine veterans organizations have formed a "Save the Silversides" fund and have begun soliciting tax-deductible donations through veterans groups and military publications. They based their plans on the dry-dock overhaul of , a memorial in Manitowoc, Wisconsin, which cost US $500,000 in 1996.